General information for g12190.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Elongation of very long chain fatty acids protein.
Parent gene
- The parent gene g12190 is located on chr_1: 21659344..21665041 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_1 | g12190 | g12190.t1 | TTS | g12190.t1 | 21658510 | 21658510 |
| chr_1 | g12190 | g12190.t1 | isoform | g12190.t1 | 21658682 | 21662062 |
| chr_1 | g12190 | g12190.t1 | exon | g12190.t1.exon1 | 21658682 | 21659145 |
| chr_1 | g12190 | g12190.t1 | cds | g12190.t1.CDS1 | 21658682 | 21659145 |
| chr_1 | g12190 | g12190.t1 | exon | g12190.t1.exon2 | 21659325 | 21659460 |
| chr_1 | g12190 | g12190.t1 | cds | g12190.t1.CDS2 | 21659325 | 21659460 |
| chr_1 | g12190 | g12190.t1 | exon | g12190.t1.exon3 | 21659571 | 21659759 |
| chr_1 | g12190 | g12190.t1 | cds | g12190.t1.CDS3 | 21659571 | 21659759 |
| chr_1 | g12190 | g12190.t1 | exon | g12190.t1.exon4 | 21661922 | 21662062 |
| chr_1 | g12190 | g12190.t1 | cds | g12190.t1.CDS4 | 21661922 | 21662062 |
| chr_1 | g12190 | g12190.t1 | TSS | g12190.t1 | NA | NA |
Sequences
>g12190.t1 Gene=g12190 Length=930
ATGGATGCTCTAAACAAAATTAGTGCCACATGGCAAGACTTAATGGACAACAAGTCCGAT
CCAAGAACGACAAATTGGTTCCTTATGTCATCGCCACTTCCCACTGTGATGATCTGCCTT
ACATATGTTTATTTAGTCAAGATAGTTGGTCCTGCGCTTATGGAAAATCGAAAGCCATTT
CAGTTAAGAAAAATCATTGTAGTTTATAATTTTCTGCAAGTACTACTGAGTGCTTGGCTG
TTTTGGGGTTTGGGAAAATCGGGATGGTTCACAAATTATAGTTACAGATGTCAACCAGTA
GATTTATCTTATAGTGCACAAGCCATACAGATGACACACTTTTGTTGGTGGTATTACTTC
AGTAAATTTACAGAGTTCTTTGACACATTTTTCTTTGTTTTGAGAAAAAGATATGATCAA
GTTTCAACTTTGCATGTAATTCATCATGGAATTATGCCTTTTAGTGTATGGTGGGGAGTG
AAATTCATGCCTGGCGGTCACAGCACCTTCTTTGGACTCCTCAACACATTTGTGCATATC
ATAATGTATACTTATTATATGTTAGCTGCAATGGGACCACAAGTTCAAAAATATCTTTGG
TGGAAAAAATATCTAACAATTTTGCAGATGATCCAATTTGTTGGAATTTTTACTCATTGC
TTCCAACTGATCTTCCATAATCCCTGCAATTACTCTTATATTTTTGTATATTGGATTGGT
GGTCATGGTGTGCTGTTTTATTTCCTCTTTAGAAGCTTCTATCAACAAGCTTATGTGGCG
AAATCAAAATCAGTAAAAAATGATGAACCAAATGACAAAAAGACATTAATTGTAGATGAC
AATGAAAATATTGTAGAATACAAGAAACATTATGAGACAAAAAGAGACTCAATAACACAG
ATTAATAAGGCACTAGCGAAGCATCTTTAA
>g12190.t1 Gene=g12190 Length=309
MDALNKISATWQDLMDNKSDPRTTNWFLMSSPLPTVMICLTYVYLVKIVGPALMENRKPF
QLRKIIVVYNFLQVLLSAWLFWGLGKSGWFTNYSYRCQPVDLSYSAQAIQMTHFCWWYYF
SKFTEFFDTFFFVLRKRYDQVSTLHVIHHGIMPFSVWWGVKFMPGGHSTFFGLLNTFVHI
IMYTYYMLAAMGPQVQKYLWWKKYLTILQMIQFVGIFTHCFQLIFHNPCNYSYIFVYWIG
GHGVLFYFLFRSFYQQAYVAKSKSVKNDEPNDKKTLIVDDNENIVEYKKHYETKRDSITQ
INKALAKHL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12190.t1 | PANTHER | PTHR11157 | FATTY ACID ACYL TRANSFERASE-RELATED | 4 | 281 | 1.2E-143 |
| 3 | g12190.t1 | PANTHER | PTHR11157:SF151 | ELONGATION OF VERY LONG CHAIN FATTY ACIDS PROTEIN | 4 | 281 | 1.2E-143 |
| 1 | g12190.t1 | Pfam | PF01151 | GNS1/SUR4 family | 28 | 264 | 1.9E-59 |
| 18 | g12190.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 25 | - |
| 22 | g12190.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 26 | 45 | - |
| 13 | g12190.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 46 | 64 | - |
| 24 | g12190.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 65 | 82 | - |
| 17 | g12190.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 83 | 101 | - |
| 20 | g12190.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 102 | 120 | - |
| 12 | g12190.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 121 | 140 | - |
| 19 | g12190.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 141 | 160 | - |
| 16 | g12190.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 161 | 171 | - |
| 23 | g12190.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 172 | 192 | - |
| 14 | g12190.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 193 | 203 | - |
| 21 | g12190.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 225 | - |
| 15 | g12190.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 226 | 230 | - |
| 25 | g12190.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 250 | - |
| 11 | g12190.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 251 | 309 | - |
| 9 | g12190.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 24 | 46 | - |
| 6 | g12190.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 66 | 85 | - |
| 5 | g12190.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 112 | 134 | - |
| 4 | g12190.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 141 | 160 | - |
| 10 | g12190.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 170 | 192 | - |
| 8 | g12190.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 204 | 226 | - |
| 7 | g12190.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 231 | 253 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016021 | integral component of membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K10250 (elongation of very long chain fatty acids protein 7)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed